[gmx-users] Doubts regarding Simulation box - Thanks

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Jan 14 06:08:58 CET 2011


> So according to this my minimal box size should be
> 0.6nm in order to avoid PBS effects and due to the
> water effects i have to set it 1nm or higher.

Well, not box size, but the distance from the solute to the box wall :)

> So this rule is irrespective of the box type we choose
> isnt it?

Yes. You want to be sure to have at least the minimal distance between
images, i.e. two times the distance from the solute to the wall,

> I got the clue for my second question.

Good :)



Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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